The rapid urbanization has significantly impacted the stability of urban ecosystems. Exploring the spatiotemporal evolution characteristics of ecological resilience and its interaction with urbanization is crucial for achieving sustainable urban development. Taking the Chengdu-Chongqing urban agglomeration as an example, an evaluation framework for ecological resilience is constructed from three dimensions: "resistance-adaptability-recoverability." The interaction effect between urbanization and ecological resilience is measured using a coupling coordination model, followed by simulations of the spatial distribution of ecological resilience under two scenarios—natural development and farmland protection—in 2035. The research findings are as follows: (1) From 2010 to 2020, the level of ecological resilience in the Chengdu-Chongqing urban agglomeration fluctuated and declined, with a spatial distribution pattern of central concentration and peripheral dispersion. High and low levels of ecological resilience showed clustering characteristics. There were significant differences in ecological resilience levels among cities, with the gap widening. (2) The interactive effects between different types of urbanization and ecological resilience vary significantly. Specifically, population urbanization, spatial urbanization, and social urbanization exhibit trade-off effects with ecological resilience, whereas economic urbanization demonstrates a synergistic effect with ecological resilience. (3) In 2035, the level of ecological resilience in the urban agglomeration based on land use expansion under the natural development scenario is higher than that under the farmland protection scenario, mainly due to the significantly higher resistance level under the natural development scenario compared to the farmland protection scenario.